Strain Passport - Pseudomonas fluorescens

1. Taxonomy

Taxonomy
Domain Bacteria
Phylum Proteobacteria
Class Gammaproteobacteria
Order Pseudomonadales
Family Pseudomonadaceae
Genus Pseudomonas_E
Species Pseudomonas_E fluorescens

2. Assembly Statistics

Assembly Statistics
MAGID MAG15
Size (bp) 6260555
N.contigs 281
GC (%) 60.2
N50 (bp) 37481
Coding Density 88.8
N.CDSs 5697
Genome Completeness
Completeness 99.25
Contamination 1.12
Strain heterogeneity 20.00

3. Metabolism and Function (KEGG)

KEGG Function Annotation

Pseudomonas fluorescens KEGG Functional Classification

KEGG Resistome

name Type Level1 Level2 Description KO
ko01504 Gene variants Aminoglycoside resistance genes O-Phosphotransferases K19300 aph3-II; aminoglycoside 3’-phosphotransferase II [EC:2.7.1.95] K19300
ko01504 Gene variants Aminoglycoside resistance genes O-Phosphotransferases K04343 strB; streptomycin 6-kinase [EC:2.7.1.72] K04343
ko01504 Gene variants Macrolide resistance genes Transporters K08217 mef; MFS transporter, DHA3 family, macrolide efflux protein K08217
ko01504 Gene variants Quinolone resistance genes Other K18555 qnr, mcbG; fluoroquinolone resistance protein K18555
ko01504 Gene sets beta-Lactam resistance modules Imipenem resistance, repression of porin OprD [MD:M00745] K18072 parS; two-component system, OmpR family, sensor kinase ParS [EC:2.7.13.3] K18072
ko01504 Gene sets beta-Lactam resistance modules Imipenem resistance, repression of porin OprD [MD:M00745] K18073 parR; two-component system, OmpR family, response regulator ParR K18073
ko01504 Gene sets beta-Lactam resistance modules Imipenem resistance, repression of porin OprD [MD:M00745] K07644 cusS, copS, silS; two-component system, OmpR family, heavy metal sensor histidine kinase CusS [EC:2.7.13.3] K07644
ko01504 Gene sets beta-Lactam resistance modules Imipenem resistance, repression of porin OprD [MD:M00745] K07665 cusR, copR, silR; two-component system, OmpR family, copper resistance phosphate regulon response regulator CusR K07665
ko01504 Gene sets beta-Lactam resistance modules Imipenem resistance, repression of porin OprD [MD:M00745] K18297 mexT; LysR family transcriptional regulator, mexEF-oprN operon transcriptional activator K18297
ko01504 Gene sets beta-Lactam resistance modules Imipenem resistance, repression of porin OprD [MD:M00745] K18093 oprD; imipenem/basic amino acid-specific outer membrane pore [EC:3.4.21.-] K18093
ko01504 Gene sets CAMP resistance modules Cationic antimicrobial peptide (CAMP) resistance, dltABCD operon [MD:M00725] K03367 dltA; D-alanine–poly(phosphoribitol) ligase subunit 1 [EC:6.1.1.13] K03367
ko01504 Gene sets CAMP resistance modules Cationic antimicrobial peptide (CAMP) resistance, lysyl-phosphatidylglycerol (L-PG) synthase MprF [MD:M00726] K14205 mprF, fmtC; phosphatidylglycerol lysyltransferase [EC:2.3.2.3] K14205
ko01504 Gene sets CAMP resistance modules Cationic antimicrobial peptide (CAMP) resistance, protease PgtE [MD:M00744] K07637 phoQ; two-component system, OmpR family, sensor histidine kinase PhoQ [EC:2.7.13.3] K07637
ko01504 Gene sets CAMP resistance modules Cationic antimicrobial peptide (CAMP) resistance, protease PgtE [MD:M00744] K07660 phoP; two-component system, OmpR family, response regulator PhoP K07660
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexAB-OprM [MD:M00718] K03585 acrA, mexA, adeI, smeD, mtrC, cmeA; membrane fusion protein, multidrug efflux system K03585
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexAB-OprM [MD:M00718] K18138 acrB, mexB, adeJ, smeE, mtrD, cmeB; multidrug efflux pump K18138
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexAB-OprM [MD:M00718] K18139 oprM, emhC, ttgC, cusC, adeK, smeF, mtrE, cmeC, gesC; outer membrane protein, multidrug efflux system K18139
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexEF-OprN [MD:M00641] K18297 mexT; LysR family transcriptional regulator, mexEF-oprN operon transcriptional activator K18297
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexEF-OprN [MD:M00641] K18298 mexE; membrane fusion protein, multidrug efflux system K18298
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexEF-OprN [MD:M00641] K18300 oprN; outer membrane protein, multidrug efflux system K18300
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexJK-OprM [MD:M00642] K18301 mexL; TetR/AcrR family transcriptional regulator, mexJK operon transcriptional repressor K18301
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexJK-OprM [MD:M00642] K18302 mexJ; membrane fusion protein, multidrug efflux system K18302
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexJK-OprM [MD:M00642] K18303 mexK; multidrug efflux pump K18303
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexJK-OprM [MD:M00642] K18139 oprM, emhC, ttgC, cusC, adeK, smeF, mtrE, cmeC, gesC; outer membrane protein, multidrug efflux system K18139
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexXY-OprM [MD:M00643] K18139 oprM, emhC, ttgC, cusC, adeK, smeF, mtrE, cmeC, gesC; outer membrane protein, multidrug efflux system K18139
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MexPQ-OpmE [MD:M00769] K19591 cueR; MerR family transcriptional regulator, copper efflux regulator K19591
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump AdeABC [PATH:map01501] [MD:M00649] K18143 adeS; two-component system, OmpR family, sensor histidine kinase AdeS [EC:2.7.13.3] K18143
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump AdeABC [PATH:map01501] [MD:M00649] K18144 adeR; two-component system, OmpR family, response regulator AdeR K18144
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump AcrEF-TolC [MD:M00696] K12340 tolC, bepC, cyaE, raxC, sapF, rsaF, hasF; outer membrane protein K12340
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MdtEF-TolC [MD:M00697] K07690 evgA, bvgA; two-component system, NarL family, response regulator EvgA K07690
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump MdtEF-TolC [MD:M00697] K12340 tolC, bepC, cyaE, raxC, sapF, rsaF, hasF; outer membrane protein K12340
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump BpeEF-OprC [MD:M00698] K18900 bpeT; LysR family transcriptional regulator, regulator for bpeEF and oprC K18900
ko01504 Gene sets Multipdrug resistance modules Multidrug resistance, efflux pump BpeEF-OprC [MD:M00698] K18903 oprC, opcM; outer membrane protein, multidrug efflux system K18903

KEGG Toxins

name Type Level1 Level2 Description KO
ko02042 Type II toxins: Membrane damaging toxins Pore-forming toxins, Other K03699 tlyC; magnesium and cobalt exporter, CNNM family tlyC; magnesium and cobalt exporter, CNNM family K03699
ko02042 Type II toxins: Membrane damaging toxins Pore-forming toxins, Other K11016 shlA, hhdA, hpmA; hemolysin shlA, hhdA, hpmA; hemolysin K11016
ko02042 Type II toxins: Membrane damaging toxins Pore-forming toxins, Other K11017 shlB, hhdB, hpmB; hemolysin activation/secretion protein shlB, hhdB, hpmB; hemolysin activation/secretion protein K11017
ko02042 Type II toxins: Membrane damaging toxins Pore-forming toxins, Other K11068 hlyIII; hemolysin III hlyIII; hemolysin III K11068
ko02042 Type II toxins: Membrane damaging toxins Toxins that enzymatically damage the membrane K01114 plc; phospholipase C [EC:3.1.4.3] plc; phospholipase C [EC:3.1.4.3] K01114
ko02042 Type II toxins: Membrane damaging toxins Toxins that enzymatically damage the membrane K16638 exoU; exoenzyme U exoU; exoenzyme U K16638

KEGG Bacterial Virulence

GeneID KO Description PFAM
MAG15_MEIOIK_01485 K07345 major type 1 subunit fimbrin (pilin) Fimbrial protein [PF00419.23]…
MAG15_MEIOIK_01495 K07347 outer membrane usher protein Outer membrane usher protein [PF00577.23]…
MAG15_MEIOIK_11455 K07345 major type 1 subunit fimbrin (pilin) Type-1 fimbrial protein, A [PF16970.8]…
MAG15_MEIOIK_11465 K07347 outer membrane usher protein Outer membrane usher protein [PF00577.23]…
MAG15_MEIOIK_11470 K07345 major type 1 subunit fimbrin (pilin) Fimbrial protein [PF00419.23]…
MAG15_MEIOIK_12015 K07347 outer membrane usher protein Outer membrane usher protein [PF00577.23]…
MAG15_MEIOIK_13535 K03596 GTP-binding protein LepA GTP-binding protein LepA C-terminus [PF06421.15]…
MAG15_MEIOIK_13995 K15125 filamentous hemagglutinin TPS secretion domain [PF05860.16]…
MAG15_MEIOIK_14000 K07326 hemolysin activation/secretion protein Haemolysin secretion/activation protein ShlB/FhaC/HecB [PF03865.16]…
MAG15_MEIOIK_20695 K07326 hemolysin activation/secretion protein Haemolysin secretion/activation protein ShlB/FhaC/HecB [PF03865.16]…
MAG15_MEIOIK_20700 K15125 filamentous hemagglutinin Possible hemagglutinin (DUF637) [PF04830.16]…
MAG15_MEIOIK_22200 K08303 U32 family peptidase [EC:3.4.-.-] Peptidase family U32 [PF01136.22]…

Carbon Metabolism

Nitrogen Metabolism

4. Expert systems

AMRFinderPlus Antimicrobial Resistance

AMRFinderPlus
locus pscc.product gene_family class subclass
MEIOIK_03380 Glutathione transferase fos FOSFOMYCIN FOSFOMYCIN
MEIOIK_20675 Beta-lactamase ampC BETA-LACTAM BETA-LACTAM

Virulence factors (VFDB)

VFDB
VFG.x VFCID VFcategory VFSubcategory psc.uniref90_id
VFG000121 VFC0271 Biofilm Csu fimbriae UniRef90_G9HQL5
VFG002069 VFC0086 Effector delivery system T2SS UniRef90_A0A1T3A5T5
VFG002070 VFC0086 Effector delivery system T2SS UniRef90_Q9I748
VFG043016 VFC0204 Motility Polar flagella UniRef90_A0A0F4U0N1

5. BacDive

BacDive
Species Pseudomonas fluorescens
ncbi_taxid 294
taxid_matching_level species
type_strain no
medium_name NUTRIENT AGAR (DSMZ Medium 1)
medium_link NA
strain_history NA
gram NA
length NA
width NA
motility NA
oxygen_tolerance NA
spore NA
aggregation_score NA
GC_content NA
antibiotic_resistance_chebi NA
antibiotic_resistance_metabolite NA

6. Publications

7. U.S. Patents

First 10 patents out of 92

patent_number patent_title
10041102 Expression of mammalian proteins in Pseudomonas fluorescens
10201162 Pseudomonas species having weed suppressive activity and benign soil survival traits for annual grass weed management
10807919 Biofertilizer to increase agricultural yield
10982185 Desiccation resistant pseudomonad strains and treatment of agricultural maladies therewith
11098285 Virulent Pseudomonas fluorescens phage FPf1901, and phage FPf901 preparation and application thereof
3977943 Antibiotics
4071536 Antibiotics
4205002 Antibacterial compounds
4226880 Antibacterial compounds
4228191 Microbiological decaffeination of aqueous liquids